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Stephen is loosely based on the theoretical physicist Stephen Hawking. Hawking is famous for developing theorems based on black hole singularity and the transfer of items entering a black hole to another universe. He has since developed a new theorem which discounts the transfer to another universe, instead opting for the idea that information would be spit back out of the black hole in a garbled state.

Stephen is a brilliant computer programmer who is the main architect of the Terminal System project, a revolutionary technology which allowed instantaneous travel through computer networks. However, during one of those experiments, a terminal accidentally connected to the Expanse, causing a demon to travel through. The supernatural being tried to communicate with Stephen, but as Stephen wasn't able to comprehend its language, it eventually got hostile and attacked, resulting in the crippling of Stephen.

This event ended up motivating Stephen in developing the Demon Summoning Program, a computer file that, once downloaded in a COMP, will allow its user to translate the demon language, allowing for proper communication. It also possesses an auto-map and stores demons on its memory plate function, as Stephen hoped that someone would one day be able to use it to ally himself with demons to avert the obliteration of Tokyo by the upcoming war of the rising Messian and Gaean factions.

Thus, he sent the Demon Summoning Program through e-mail to as many people as possible, before being captured by Gotou's forces and imprisoned in Echo Building; where he would meet the protagonist for the very first time. After this, he only makes minor appearances through the game, mostly to upgrade the protagonist's computer as well as the Demon Summoning Program, allowing the hero to store and summon more demons at the same time.

Stephen is first mentioned when some drinkers at a bar informs Hawk that a "guy in a wheelchair" has been seen by numerous fighters while Virtual Battling, and that this phenomenon was not supposed to be part of the program. While training in the virtual world, Aleph himself is approached by the mysterious man who, after introducing himself, predicts that great calamities are about to befall Tokyo Millennium, saying that he has been waiting for strong warriors to appear at the various public Virtual Battlers scattered through town as to be able to give them what he calls a "Demon Summoning Program"; stating that if humanity doesn't learn how to use the power of the demons as their own, they will be destroyed by it. It is mainly through this technology, uploaded into Hawk's Arm Terminal, that he can communicate, recruit, and summon different demons.

Through the remainder of the game, Stephen can been seen on various other optional appearances, all in Virtual Battlers of different districts of both Tokyo Millennium and the Underworld. It is over these meetings that Stephen is able to grant Aleph with different improvements and upgrades to his Demon Summoning Program, giving him the ability to stock more and more minions (to the maximum capability of twelve) through the use of a compression algorithm that, according to him, reduces the size of demon data that is able to be simultaneously stored inside a computer. The Devil Analyze program and the Identification System (used to show information about specific demons and certain items, respectively) were both also engineered by Stephen.

He appears much later, this time in Yesod, one of the multiple districts of the Abyss. There, he activates for Aleph the Terminal technology used in the Abyss, so that he can save the game and teleport himself whenever he likes. In the Neutral Route he teleports Aleph to Eden after you defeat the dragon Kuzuryu.

Stephen appears in silhouette during a cutscene that describes the events of Shin Megami Tensei. His Demon Summoning Program has been adopted as the main weapon of the Demon Busters, granting them the ability to summon and store demons. Snakeman and Madam Justice both mention having received help from Stephen in the past.

Stephen returns as a guide to the protagonist, giving hints throughout the game. His appearance is said to be mere references to previous games in the series. He first appears in Alraune's Domain and introduces himself to the prentice Samurai. He mentions that the girl has taken an interest in Flynn. He offers to heal their wounds in a room further in if they are injured.

He appears in the dream Flynn has after the Lilim incapacitate him and tells him that she wants to see him to the east, then vanishes. In Naraku he appears at the Temporary Scaffolding floor, updates the devil summoning program and disappears again.

If Flynn remains neutral throughout the game, he meets Stephen at the Monochrome Forest, who tells him to defeat the White. He explains that the girl is, in fact, the goddess of Tokyo, and that by lifting the ceiling over Tokyo, that she may be restored to her original form.

In the DLC Challenge QuestFor the Past... For the Future, Stephen is met in the Expanse, which, he explains, is a place that transcends time. He takes Flynn to the past, to the day the ceiling formed over Tokyo to protect it from incoming missiles, and explains the events leading up to that day:

When the Yamato Perpetual Reactor connected to the Expanse, it allowed demons to come into the world. This led to wars for control between the angels and demons, a world war among humanity, and the launch of the worst weapons known to man. He tells Flynn that he must help Masakado regain his senses and become the ceiling, and warns that any future Tokyo will fade into only a possibility if the city is destroyed.

After Masakado's restoration and the rise of the Firmament, Stephen states that history will now continue along the path they remember, with Mikado's formation and Flynn's eventual birth, and returns Flynn to his own time, thanking him and Burroughs for saving everyone.

Stephen appears to the cast from time to time, guiding them on their quest and occasionally lending indirect assistance - most notably while disguised as Dr. Matsuda when developing measures to counter Shesha. His main motive appears to be to help restore the Goddess of Tokyo after her body is damaged.

At the final chapter of the game, he appears to Nanashi to explain how humans and gods interact, and shows the party the way to YHVH's Universe, with the intent of defeating the Creator in order to either usher in true freedom for humanity or to pave the way for the new universe.

Although mysterious and often appearing as a neutral figure in the background, Stephen reveals a more ruthless side in his desire to see human potential on Dagda's route. There he sends the united forces of humanity intentionally to their doom, knowing they would fail and to serve as a lesson to ensure Nanashi will not back down from his current resolve. He also gives multiple warnings to the new Creator who still retains his humanity, leaving to chase the Goddess of Tokyo after warning him of Messiahs and the fates that befell Krishna, Lucifer, Merkabah, and YHVH.

Stephen is the one behind the DLC quest "Messiahs in the Diamond Realm". He summons The Hero, Aleph, the Demi-fiend, and an alternate version of Flynn into the Diamond Realm, as a means to save them from YHVH's attempts to destroy them. He then calls Nanashi into the Diamond Realm, instructing him to find the other four Messiahs and guide them back to their worlds. He has one in his possession - that of The Hero's, and has Nanashi find the remaining three first.

Once the other three Messiahs are gathered, En no Ozuno unlocks a door that allows Nanashi meets with Stephen, who instructs him to use his powers of observation to have the Hero regain his form. To this end, Stephen does battle with Nanashi, hoping to have the Hero remember who he is.

As the Hero reforms, the remaining Messiahs burst into the room. Stephen then gets out of his wheelchair, explaining his motives. He had sensed that humans have the potential to exceed the Axiom, and thus extended a chance for salvation to them. He then does battle with Nanashi's party and the four Messiahs, giving them a chance to show whether it was worth saving them and defying the Axiom's laws. He unleashes his full power as the game's Ultimate Boss.

The second battle is easily the hardest fight in the game. Stephen has an estimated 100,000 HP, and initially resists everything. However, akin to the battle with YHVH, the player alternates between Nanashi's party and the Messiahs, and the Hero and Aleph possess skills that can reduce Stephen's resistances and potentially open up weaknesses. Stephen also possesses very strong moves - Pair Production fully buffs himself and gives him smirk; Particle Annihilation fully debuffs the active party; Reboot code wipes the party of all buffs and effects up to and including Charge, smirk and Doping. His most dangerous attack is Singularity Wave, an almighty attack that inflicts several thousand damage which can immediately kill any combatant without excessive HP reserves. While it can be dodged, the attack landing on Nanashi on Apocalypse difficulty can completely ruin the fight.

All his elemental attacks pierce resistances, but his physical attacks don't, so bringing phys-immune demons to the fight can easily snatch away his turns. Refrain from fully buffing yourself or debuffing him - i.e. keep him at -2 on all stats and you on +2 on all of yours - as having excessive buffs or debuffs can cause him to use Dekunda, Reboot Code, Pair Production and Particle Annihilation more often.

Between the Messiahs, it is best to have The Hero and Aleph focus on reducing Stephen's weaknesses to make it easier for both teams to do damage to him. Making Stephen weak to physical attacks will allow both teams to get a long string of free Press Turns. The Demi-Fiend is the party's main damage dealer, as his Deadly Fury has a very high critical rate, allowing him to easily smirk and fire off double-power Freikugels. Flynn is largely reduced to support, being the party's only source of Mediarahan, but on odd turns he can strike any elemental weaknesses or fire off Smile Charged Antichthons.

Upon defeat, Stephen applauds the Messiahs for demonstrating their power, and leaves. A wormhole opens, allowing each Messiah to return to their universe and set right what went wrong. En no Ozuno bids Nanashi farewell as the quest is complete.

"While the details are unclear, Matsuda was allegedly a video game programmer before eventually being scouted by Fujiwara to join the Hunter Association's research and developenent team."

—Shin Megami Tensei IV Apocalypse Notes, entry - "Dr. Matsuda"

The human guise created by Stephen and implemented into the Hunter Association to aid Nanashi. He builds the Shesha Radar that tracks Shesha's location while in the form of this 60 year old man, having rewritten the memories of the Association into believing he was always a member. Upon the radar's destruction at the hands of Shesha-Flynn he disappears and removes all memories of his existence from the Hunters Association, leaving only the memories of Nanashi unchanged.

Kazuyuki Yamai (producer of Shin Megami Tensei IV Apocalype) stated in an interview that Stephen is the same person across the series, traveling across time and space to the various universes in which each game occurs. In the process he has become a Buddha figure alongside Mido and Saint Germain.

Though not appearing in person, one of the software installations for the COMP in Soul Hackers is named "Steven", likely after him. It removes the level limit during COMP Fusion in a New Game Plus.

In the DLC Boss Battle against him in Shin Megami Tensei IV Apocalypse, the Hero notes that magnetite is flowing out of Stephen.